Input and runtime details for job 1765463 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
193	0.04043	0.6177	b1180	ycgM	-6.42	0.210248	289 -- 296	47 -- 54	putative isomerase/hydrolase	_____________288______297\n_____________\|________\|\n5'-GAU...ACAUA________AUGG-3'\n______________UUAAAGAG\n______________\|:\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	290 -- 296	47 -- 53	-7.63974 kcal/mol	0.325787 kcal/mol	0.897871 kcal/mol	288 297@LB@ \| \|@LB@5'-GAU...ACAUA AUGG-3'@LB@ UUAAAGAG@LB@ \|:\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -6.42 kcal/mol@LB@Hybridization Energy -7.63974 kcal/mol@LB@Unfolding Energy - mRNA 0.325787 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 289 -- 296@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 47 -- 53@LB@
197	0.04129	0.6177	b1205	ychH	-8.72	0.074776	153 -- 162	43 -- 52	DUF2583 family putative inner membrane protein	_____________152________163\n_____________\|__________\|\n5'-CAA...AUAAG__________AUUCC...UAC-3'\n______________GAAGAGGGGU\n______________:\|\|\|\|\|\|::\|\n______________UUUCUCCUUA\n3'-UUU...GGCAG__________AAGUA...ACA-5'\n_____________\|__________\|\n_____________53_________42\n	156 -- 162	43 -- 49	-11.7568 kcal/mol	2.17132 kcal/mol	0.865937 kcal/mol	152 163@LB@ \| \|@LB@5'-CAA...AUAAG AUUCC...UAC-3'@LB@ GAAGAGGGGU@LB@ :\|\|\|\|\|\|::\|@LB@ UUUCUCCUUA@LB@3'-UUU...GGCAG AAGUA...ACA-5'@LB@ \| \|@LB@ 53 42@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.7568 kcal/mol@LB@Unfolding Energy - mRNA 2.17132 kcal/mol@LB@Unfolding Energy - sRNA 0.865937 kcal/mol@LB@@LB@Position - mRNA 153 -- 162@LB@Position - sRNA 43 -- 52@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 43 -- 49@LB@
102	0.02032	0.6177	b1267	yciO	-10.56	0.031637	188 -- 197	44 -- 53	putative RNA binding protein	_____________187________198\n_____________\|__________\|\n5'-GCG...CACCA__________AUUAU...CAA-3'\n______________CAGAGAGGGA\n______________\|\|:\|\|\|\|\|:\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	46 -- 52	-13.8947 kcal/mol	2.40877 kcal/mol	0.927997 kcal/mol	187 198@LB@ \| \|@LB@5'-GCG...CACCA AUUAU...CAA-3'@LB@ CAGAGAGGGA@LB@ \|\|:\|\|\|\|\|:\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.8947 kcal/mol@LB@Unfolding Energy - mRNA 2.40877 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 188 -- 197@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@LB@
180	0.03697	0.6177	b1325	ycjG	-6.24	0.226397	189 -- 195	47 -- 53	L-Ala-D/L-Glu epimerase	_____________188_____196\n_____________\|_______\|\n5'-AAG...GACAA_______UAAAG...AAC-3'\n______________CAAGGAG\n______________\|\|\|:\|\|\|\n______________GUUUCUC\n3'-UUU...GGGCA_______CUUAA...ACA-5'\n_____________\|_______\|\n_____________54______46\n	189 -- 195	47 -- 53	-8.11062 kcal/mol	0.981925 kcal/mol	0.886139 kcal/mol	188 196@LB@ \| \|@LB@5'-AAG...GACAA UAAAG...AAC-3'@LB@ CAAGGAG@LB@ \|\|\|:\|\|\|@LB@ GUUUCUC@LB@3'-UUU...GGGCA CUUAA...ACA-5'@LB@ \| \|@LB@ 54 46@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -8.11062 kcal/mol@LB@Unfolding Energy - mRNA 0.981925 kcal/mol@LB@Unfolding Energy - sRNA 0.886139 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 47 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 47 -- 53@LB@
13	0.003065	0.593	b4529	ydbJ	-10.82	0.027981	161 -- 194	44 -- 78	DUF333 family putative lipoprotein	_____________160___________________________________195\n_____________\|_____________________________________\|\n5'-GCA...UAUUU________________________AA__UC_______GAAAA...GUU-3'\n______________AUGG_CGGUGUCGU__UUGGCUUG__GA__AGAGGAA\n______________\|\|\|\|_\|::\|:\|\|\|:__\|\|\|\|\|::\|__:\|__\|\|\|\|\|\|\|\n______________UACC_GUUAUAGCG__AACCGGGC__UU__UCUCCUU\n_____3'-UUUUUU____G_________AU________AG___________AAAGU...ACA-5'\n_____________\|_____________________________________\|\n_____________79____________________________________43\n	188 -- 194	44 -- 50	-34.9495 kcal/mol	10.5981 kcal/mol	13.5333 kcal/mol	160 195@LB@ \| \|@LB@5'-GCA...UAUUU AA UC GAAAA...GUU-3'@LB@ AUGG CGGUGUCGU UUGGCUUG GA AGAGGAA@LB@ \|\|\|\| \|::\|:\|\|\|: \|\|\|\|\|::\| :\| \|\|\|\|\|\|\|@LB@ UACC GUUAUAGCG AACCGGGC UU UCUCCUU@LB@ 3'-UUUUUU G AU AG AAAGU...ACA-5'@LB@ \| \|@LB@ 79 43@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -34.9495 kcal/mol@LB@Unfolding Energy - mRNA 10.5981 kcal/mol@LB@Unfolding Energy - sRNA 13.5333 kcal/mol@LB@@LB@Position - mRNA 161 -- 194@LB@Position - sRNA 44 -- 78@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
77	0.01626	0.6177	b1414	ydcF	-7.59	0.125301	189 -- 198	44 -- 53	DUF218 superfamily protein SAM-binding	_____________188________199\n_____________\|__________\|\n5'-GGU...AACGA__________CCAUG...UGC-3'\n______________UAAGGAGGAA\n______________:\|\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	192 -- 198	44 -- 50	-11.4771 kcal/mol	2.95852 kcal/mol	0.927997 kcal/mol	188 199@LB@ \| \|@LB@5'-GGU...AACGA CCAUG...UGC-3'@LB@ UAAGGAGGAA@LB@ :\|\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -11.4771 kcal/mol@LB@Unfolding Energy - mRNA 2.95852 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 189 -- 198@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
119	0.02381	0.6177	b1434	ydcN	-8.41	0.086264	87 -- 94	43 -- 50	putative DNA-binding transcriptional regulator	_____________86_______95\n_____________\|________\|\n5'-CGG...UGGGU________AGAAA...CUA-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	88 -- 94	43 -- 49	-10.2233 kcal/mol	0.967994 kcal/mol	0.845564 kcal/mol	86 95@LB@ \| \|@LB@5'-CGG...UGGGU AGAAA...CUA-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -10.2233 kcal/mol@LB@Unfolding Energy - mRNA 0.967994 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 87 -- 94@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 43 -- 49@LB@
42	0.008125	0.6129	b2431	yfeX	-9.88	0.043594	266 -- 278	44 -- 56	porphyrinogen oxidase cytoplasmic	_____________265___________279\n_____________\|_____________\|\n5'-AUU...GCCAA___G_________GUUGA...CCA-3'\n______________CGU_AAAGGGGAA\n______________\|\|\|_\|\|\|\|:\|\|\|\|\n______________GCA_UUUCUCCUU\n3'-UUU...ACCGG___G_________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________57____________43\n	272 -- 278	44 -- 50	-15.4775 kcal/mol	4.65199 kcal/mol	0.948902 kcal/mol	265 279@LB@ \| \|@LB@5'-AUU...GCCAA G GUUGA...CCA-3'@LB@ CGU AAAGGGGAA@LB@ \|\|\| \|\|\|\|:\|\|\|\|@LB@ GCA UUUCUCCUU@LB@3'-UUU...ACCGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -15.4775 kcal/mol@LB@Unfolding Energy - mRNA 4.65199 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 266 -- 278@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 44 -- 50@LB@
72	0.015	0.6177	b2513	yfgM	-10.40	0.034106	179 -- 190	45 -- 55	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________178__________191\n_____________\|____________\|\n5'-GGC...ACUGG________A___GAAGG...UUG-3'\n______________GUUAAGGA_GGA\n______________\|\|:\|\|:\|\|_\|\|\|\n______________CAGUUUCU_CCU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	180 -- 186	48 -- 54	-12.2699 kcal/mol	0.940443 kcal/mol	0.930875 kcal/mol	178 191@LB@ \| \|@LB@5'-GGC...ACUGG A GAAGG...UUG-3'@LB@ GUUAAGGA GGA@LB@ \|\|:\|\|:\|\| \|\|\|@LB@ CAGUUUCU CCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -12.2699 kcal/mol@LB@Unfolding Energy - mRNA 0.940443 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 190@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 48 -- 54@LB@
186	0.03879	0.6177	b2898	ygfZ	-4.98	0.377094	224 -- 230	51 -- 57	iron-sulfur cluster repair protein plumbagin resistance	_____________223_____231\n_____________\|_______\|\n5'-CGU...CCUCC_______CCUAC...CUG-3'\n______________CCGUCAG\n______________\|\|\|\|\|\|:\n______________GGCAGUU\n3'-UUU...AACCG_______UCUCC...ACA-5'\n_____________\|_______\|\n_____________58______50\n	224 -- 230	51 -- 57	-9.02345 kcal/mol	1.32881 kcal/mol	2.71582 kcal/mol	223 231@LB@ \| \|@LB@5'-CGU...CCUCC CCUAC...CUG-3'@LB@ CCGUCAG@LB@ \|\|\|\|\|\|:@LB@ GGCAGUU@LB@3'-UUU...AACCG UCUCC...ACA-5'@LB@ \| \|@LB@ 58 50@LB@@LB@@LB@Energy -4.98 kcal/mol@LB@Hybridization Energy -9.02345 kcal/mol@LB@Unfolding Energy - mRNA 1.32881 kcal/mol@LB@Unfolding Energy - sRNA 2.71582 kcal/mol@LB@@LB@Position - mRNA 224 -- 230@LB@Position - sRNA 51 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 51 -- 57@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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